Coral Reef Baselines

The pristine or natural state of a population or community is called the baseline in conservation biology. A baseline serves as a guide for setting conservation and restoration targets. Unfortunately, scientists rarely have reliable information on baselines, because in most cases quantitative data are not collected until long after the resource has been modified. This is particularly true for marine communities which can be difficult and expensive to monitor.

A new paper in Coral Reefs “Assessing loss of coral cover on Australia’s Great Barrier Reef over two decades, with implications for longer-term trends” (Sweatman et al. 2011) tries to get at what the baseline is for the Great Barrier Reef (GBR) using the results of ecological surveys performed by the Australian Institute of Marine Science (AIMS). Sweatman et al argue that the AIMS surveys, which began in 1986, are the most reliable evidence we have and that other evidence should be ignored. However, many other scientists surveyed reefs on the GBR (for various reasons) decades before AIMS began it’s monitoring program. Three papers have collated that data and combined it with the AIMS survey data to estimate how the GBR has changed over the last 4-5 decades.

The first such paper (published in Nature by Bellwood et al 2004) included this graphic of long-term change in coral cover (the percentage of the sea floor covered by living corals – because corals facilitate so many reef inhabitants, living coral cover is a key measure of reef habitat quality and quantity, analogous to the coverage of trees as a measure of tropical forest loss):

Figure 1 (from Bellwood et al 2004). Degradation of coral reefs. a, Results of a meta-analysis of the literature, showing a decline in coral cover on the Great Barrier Reef. Each point represents the mean cover of up to 241 reefs sampled in each year. b, The recorded number of reefs on the Great Barrier Reef, Australia, substantially damaged over the past 40 yr by outbreaks of crown-of-thorns starfish (COTS) and episodes of coral bleaching.

The second study (Bruno and Selig 2007) is a meta-analyses of coral reef survey data from 2667 reefs across the Indo-Pacific performed between 1968 and 2004 (Fig. 2).

Figure 2 (from Bruno and Selig 2007). Coral cover in ten Indo-Pacific subregions in each of three periods. Plotted values are means +/- 1 SE and values above each bar are the subregional sample sizes. *=no data available

The third paper, Pandolfi et al 2003, used a variety of historical and palontological data sources in an attempt to reconstruct the longer-term, including pre-human, history of the GBR and other reefs around the world (Fig. 3).

All three studies essentially concluded that GBR coral cover and overall ecosystem health began to decline decades ago, despite the fact that the GBR is currently in better shape than many of the world’s reefs.

Sweatman et al dismiss pre-1986 data from all three studies, arguing that only AIMS survey data are suitable, and thus conclude that the GBR has changed little if at all due to human influences: “We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted”.Global climate change skeptics have frequently use a very similar approach: they rationalize cherry picking a favored data set and time interval in an attempt to show land and ocean temperatures haven’t increased, that sea ice hasn’t declined, etc.

While coral reefs in many parts of the world are in decline as a direct consequence of human pressures, Australia’s Great Barrier Reef (GBR) is unusual in that direct human pressures are low and the entire system of 2,900 reefs has been managed as a marine park since the 1980s. In spite of these advantages, standard annual surveys of a large number of reefs showed that from 1986 to 2004, average live coral cover across the GBR declined from 28 to 22%. This overall decline was mainly due to large losses in six (21%) of 29 subregions. Declines in live coral cover on reefs in two inshore subregions coincided with thermal bleaching in 1998, while declines in four mid-self subregions were due to outbreaks of predatory starfish. Otherwise, living coral cover increased in one subregion (3%) and 22 subregions (76%) showed no substantial change. Reefs in the great majority of subregions showed cycles of decline and recovery over the survey period, but with little synchrony among subregions. Two previous studies examined long-term changes in live coral cover on GBR reefs using meta-analyses including historical data from before the mid-1980s. Both found greater rates of loss of coral and recorded a marked decrease in living coral cover on the GBR in 1986, coinciding exactly with thestart of large-scale monitoring. We argue that much of the apparent long-term decrease results from combining data from selective, sparse, small-scale studies before 1986 with data from both small-scale studies and large-scale monitoring surveys after that date. The GBR has clearly been changed by human activities and live coral cover has declined overall, but losses of coral in the past 40–50 years have probably been overestimated.

For several reasons listed below, I think the main conclusion of Sweatman et al is unsupported once you consider the scientific record as a whole.

1) There is much more pre-1986 data available than Sweatman et al suggest

Our study alone (Bruno and Selig) includes data from 154 surveys of reefs across the Indo Pacific performed between just 1980 and 1982. We found that mean coral cover was 42.5% (95% CI, 39.3 and 45.6). Our analysis includes 104 GBR surveys performed between 1968 and 1983, all from published literature (see Fig. 2).

2) Baseline data from other regions indicates that historically GBR coral cover was higher than it is today (or was in 1986)

In the Caribbean a small number (a few dozen) of reliable quantitative surveys from before the early 1980s suggest the regional mean for coral cover was 30-40% (Gardner et al 2003, Schutte et al 2010: see Figs. 5 and 6 below). Because countless well trained reef scientists were working throughout the region and observed the state of reefs over the last 100 years, most Caribbean reef scientists think that historically, the regional mean of Caribbean coral cover was higher than this; probably closer to 50% (or greater). Most Caribbean reefs of this era were dominated by Acropora spp., as can be seen in the photo below from 1974:

We also have substantially more older survey data for several non-GBR Pacific regions than are available for the GBR. For example, Gomez et al surveyed more than 600 sites in the Philippines in 1981 (Gomez et al 1981). Their work clearly shows a coral baseline far higher than today in the Philippines, the GBR or anywhere else in the world. Also see Fig. 4 below from Bruno and Selig (2010) that suggests the values reported in Gomez et al are representative of other regions at the time. And note the striking difference in the distribution of coral cover values among reefs between the early 1980s and for more recent surveys. Does it look like the Indo-Pacific as a whole, the Philippines or the reefs off mainland Asia haven’t changed? NO! They clearly have. Even assuming we had no pre-1986 coral cover data for the GBR, I don’t think it is logical to assume that the GBR hasn’t followed these global trends and that it has a much lower coral cover baseline than the rest of the world.

3) The GBR was already disturbed and changing by the time the AIMS monitoring program began

AIMS began surveying a few dozen reefs along the GBR in 1986 after it became obvious that the reef ecosystem was changing due to over-fishing, sediment pollution from coastal development, ocean warming and predator outbreaks. Sweatman et al argue the values recorded by the early AIMS LTMP surveys of the late-1980s, when cover was roughly 30%, are representative of the pre-human, historical baseline. I see no reason to assume this given the well-documented anthropogenic disturbances that were already affecting the reef by then (see Fig 1).

4) Nearshore reefs were smothered by sediment from coastal development a century ago

Sweatman et al: Observations and models of the dynamics of flood plumes (Devlin et al. 2001) show that it is the inshore reefs that are frequently exposed to runoff, but these reefs constitute less than 5% of the reef area of the GBR.

Sweatman et al cite the early work of Devlin et al (2001), suggesting that only the inshore reefs are ‘frequently’ exposed to runoff, but this isn’t the case. More recent evidence from CSIRO suggests that terrestrial runoff affects a much greater area of the GBR than Sweatman et al suggest:

The remotely sensed images, taken from February 9 to 13 this year, challenge conventional thought that sediment travelling from our river systems into the GBR is captured by the longshore current and travels no more than 10 to 15km offshore, affecting only the inner Great Barrier Reef Lagoon and the inner reef corals.

Images captured by CSIRO show large plumes of terrestrial material following unconventional patterns and travelling quite fast as far as 65 to 130km, to the outer reef and, in some instances, travelling along the outer reef and re-entering the reef.

Sediment, brown and green against the blues that show 'normal' reef waters, from the Annie River (1), North Kennedy River (2), Normanby River (3) and Marrett River (4) washes into Princess Charlotte Bay, past Flinders Island (5) and along Corbett Reef (6) before being carried into the Fairway Channel (7) and into the ocean. (Credit: CSIRO: GeoScience Australia)

To quote CSIRO scientist Arnold Dekker: “A re-think is needed now that we know where flood plumes go, and what this means as organic micropollutants may be travelling to parts of the reef scientists hadn’t thought to look before”. This suggests that both mid and outer shelf reefs are impacted periodically by flood disturbance – traveling as far as 65-135km, and affecting much more than the 5% that Sweatman et al claim. Why is this important? Scientists from AIMS have already implicated nutrient runoff and and crown of thorns starfish plagues, suggesting that “frequent A. planci outbreaks on the GBR may indeed be a result of increased nutrient delivery from the land”. Further research by Jupiter et al from from the southern GBR shows that whilst the inshore reefs that are exposed to chronic high-magnitude events are clearly degraded, near shore reefs influenced by episodic, high-magnitude exposure are also showing signs of stress, with persistent high cover of fleshy macroalgae. While Sweatman et al select (cherrypick?) the stories that makes the GBR look resilient:

“There is other evidence of recovery; 6 years after bleaching, survey sites on inshore reefs in the Innisfail sector had the highest densities of juvenile corals (<10 cm diameter) of any inshore reefs of the GBR (Sweatman et al. 2007), though the densities of juvenile corals were much lower on inshore reefs in the Townsville sector.”

The inclusion of such data largely glosses over some of the other studies Sweatman et al have co-authored, showing reduced resilience and phase shifts from coral to macroalgal dominance: “In this study, 11 years of field surveys recorded the development of the most persistent coral–macroalgal phase shift (>7 years) yet observed on Australia’s Great Barrier Reef (GBR)” (read more)

5) The early GBR survey data are sound

Sweatman et al: Another concern is that the objectives of many early reef studies predisposed them to select areas of high coral cover…This change in research emphasis is likely to be reflected in the choice of study sites, with early studies selecting sites for their diverse communities and high coral cover where the study organisms are abundant and large samples can be found in a small area.

I initially thought this too, but once I got into the literature, I was reminded that the late 60s and early 70s were the heyday of disturbance ecology and most reef ecologists were community ecologists, and like their peers working in other systems, focused almost entirely on the effects of large disturbances on reef communities, e.g., Endean and Stablum 1973, Endean 1977, Connell 1978, Done 1992, Done et al. 1991, etc. Thus, if anything, I think most the early bias is in the other direction. Regardless, I agree site selection biases, both then and now, complicate long-term trend interpretation.

Sweatman et al: While the AIMS long-term data show a decline in average coral cover on GBR reefs from 28.1 to 21.7% between 1986 and 2004, two studies (Bellwood et al. 2004; Bruno and Selig 2007) based on unweighted meta-analyses have suggested that average coral cover on GBR reefs was considerably higher in the 1960s and 1970s than in the 1980s. Bellwood et al. (2004) presented a plot of mean coral cover on the GBR indicating that cover halved from ~40% in the early 1960s to ~20% in 2000, almost three times the rate of decline in the AIMS long-term monitoring data.

Bruno and Selig (2007) used information from 2,667 sites to assess change across the Indo-Pacific, including the GBR as one subregion. Based on published studies including AIMS monitoring data, they found that mean coral cover on the GBR declined by ~25% (in relative terms) from the period 1968–1983 to 1984–1996 and then was relatively stable until the end of their study period in 2004. We argue that this difference is substantially due to a change in the scale of surveys and in survey methods. The most compelling evidence for this is that, in the data sets of both studies, the annual estimates of the mean for coral cover on the GBR drop abruptly in 1986, the first year of large-scale moni- toring on the GBR, and then vary rather little around the new level in subsequent years.

The apparent abrupt drop in average coral cover on the GBR in 1986 is most probably due to the inclusion of AIMS monitoring data with cover estimates from small selected patches of reef from small-scale studies…

Like Sweatmean et al, Bruno and Selig and Bellwood et al found that at a regional scale, average coral cover on the GBR has changed little since 1984 (see Figs. 1 and 2 above). A similar pattern has been documented for the Caribbean, where substantial coral loss in the early 1980s changed to relative regional stasis since (Figs. 5A and C), i.e., a very similar pattern has been found in other regions (regardless of the scale of surveys and survey methods – also see Bruno and Selig for other Indo-Pacific examples) in which AIMS has never surveyed.

Figure 5 (From Schutte et al 2010). Annual cover values (±1 SE, closed circles, left y-axis) and site sample sizes (open circles, right y-axis) for (A) mean coral cover for all sites in the Caribbean basin (n = 1962; star: 1980, the year in which Hurricane Allen struck and white band disease outbreaks began); (B) mean macroalgal cover for all sites for which data were available (n = 875; star: 1983, the year in which the Diadema antillarum die-off began); (C) mean coral cover for all sites in the greater Caribbean except those in the Florida Keys (FLK; n = 1515); and (D) mean coral cover for all sites in the FLK subregion (n = 447)

“One of the largest monitoring programmes is operated by the Australian Institute of Marine Sciences (AIMS) (e.g. Sweatman et al. 1998). Like all large monitoring programmes, it is expensive and time-consuming. It is designed to detect changes over time in reef communities at a regional scale. There has been a massive amount of data collected in this programme, which is commendable. On the other hand, as annual surveys are run between September and May, beginning in the north and working south, seasonal changes will be difficult to separate from spatial and temporal changes. It will take perhaps 30-50 years to accumulate enough baseline data to allow useful generalizations to be made” – (Risk 1999)

The AIMS survey data presented in Sweatman et al used the “manta tow” technique; snorkelers are towed behind a boat, over a reef and visually estimate coral cover within 10m wide swaths to categories such as 0-5%, >5-10%, 10-20%, 20-30%, etc. I think the manta technique can be a valid tool for estimating crude spatio-temporal trends in coral cover. I even used the AIMS manta data in our Bruno and Selig paper, although I haven’t used it since (having spoken with several former AIMS technicians about the technique and it’s accuracy and precision). In short, Sweatman et al argue that their manta tow data is so superior to data from other sources, that only the AIMS manta data should be used to asses long-term trends in GBR state. I disagree; not to knock the AIMS manta data, but it is a visual quasi-quantitative estimate collected by technicians as compared to the pre-1986 GBR data which was all collected by renouned PhD scientists, e.g., Endean and Stablum, Connell, Done, etc, that spent their lives studying the GBR.

Furthermore, these pre-1986 GBR surveys were performed using wholly quantitative techniques such as underwater photography to estimate coral cover. I just don’t buy the argument that the AIMS-intern-manta tow data are superior to quantitative surveys by trained PhD scientists. For one, how can we know that the visual estimation of “20%” coral cover has stayed constant over time? Secondly, I really doubt any technique only capable of estimating coral cover to the nearest 10% (i.e., with such low precision) is sensitive enough to even detect the gradual decline in coral cover that has been reported for the GBR and elsewhere, e.g., ~0.5-2% a year. (Just take a look at the error bars in Fig. 2 from Sweatman et al in the Abstract above). Third, I doubt the AIMS manta surveys were run long enough to detect regional trends without including data from other sources. Given the inherent noise in the system, I usually look for 30+ years of data before I try to test for a large-scale trend.

Fourth, I think it is somewhat misleading to represent the manta tows as having far greater spatial coverage. This is only true if you compare the cumulative area of the samples. However, unlike the manta tows, quantitative benthic reef surveys include extensive independent replication and if properly designed will produce coverage estimates that are representative of the broader surrounding benthos.

Finally, I suspect that the manta technique substantially underestimates coral cover because it does not (and cannot) correct for uninhabitable (by corals) substrate that is encountered in surveying. When coral scientists use the term “coral cover”, they mean the percentage of the sea floor occupied by stony corals that is habitable by this group, i.e., hard substrate, not sand or other types of soft substrate. This is easy to factor out with other quantitative survey methods; you just divide the total coral cover by the total hard (suitable) substrate cover to calculate “coral cover”. In most cases, the hard/suitable cover is nearly 100%. But because manta tows cover wide and long swaths of reef, they inevitably include small and large patches of sand, etc, and it is impossible to do the mental math to factor this out when estimating the coverage of corals and other benthic taxa while getting pulled behind a boat in shark infested waters! (manta towing is a job for the young and immortal!) If you compare the AIMS manta data to the quantitative AIMS video transect data (~48 reefs surveyed annually) you can see this artifact: from 1994-2003 the mean coral cover from the AIMS manta tows was 21.7 +/- 0.5 (1 se) and 30.7 +/- 0.9 from the video transects. This suggests that the drop in GBR coral cover in the mid-1980s could be due to a methodological bias of the manta tow technique. Would this mean that the GBR hasn’t lost any coral or that “losses of coral in the past 40–50 years have probably been overestimated”? Only if you think that the coral cover baseline, unlike the rest of the world, for the GBR is only ~30%: as I explained above, I think this is unlikely.

Sweatman et al make a lot of noise about variation among reefs and subregions in coral cover trajectories and states. Basically, there is a high degree of spatio-temporal asynchrony in the system, as we discussed in Bruno and Selig and illustrated with this graphic:

This isn’t surprising or atypical and it doesn’t mean a long-term trend isn’t present or detectable, as Sweatman et al suggest. Climate change deniers use this argument frequently, suggesting that natural short term variation makes long-term, anthropogenically forced trends, unlikely or undetectable. This is in a sense what Sweatman et al are arguing as well. But the fact that there is great unforced spatiotemporal variation, i.e, noise or weather, does not mean that longer-term, human-induced change isn’t also happening. (Although this is indeed a big issue for many fields of global change science: how to detect slow, long-term trends in a sea of shorter term noise.)

Sweatman et al: A reef system that is stable in the long term will still show cycles of disturbance and recovery at a subregional scale

True, but so will a reef system that isn’t stable and is declining as has been shown for other regions such as the Caribbean (Schutte et al 2010).

Sweatman et al: In the kind of broad analysis presented here, reef resilience is manifested as substantial increases in coral cover following disturbance. In the great majority of sub- regions of the GBR, reefs showed both declines and sub- stantial periods of increasing living coral cover over the 19 years of surveys, evidence that many reefs retained their regenerative capacity.

This, I largely agree with. In fact, there isn’t much doubt that reefs on the GBR have not lost all their regenerative capacity, eg, see here.

Shifting baseline syndrome

In his classic 1995 paper in Trends in Ecology and Evolution, Daniel Pauly outlined his argument for shifting baseline syndrome in fisheries:

Essentially, this syndrome has arisen because each generation of fisheries scientists accepts as a baseline the stock size and species compostion that occurred at the beginning of their careers, and uses this to evaluate changes. When the next generation starts its career, the stocks have further declined, but it is the stocks at that time that serve as a new baseline. The result obviously is a gradual shift of the baseline, a gradual accommodation of the creeping disappearance of resource species, and inappropriate reference points for evaluating economic losses resulting from overfishing, or for identifying targets for rehabilitation measures.

The Sweatman et al paper is a great example of shifting baseline syndrome: coral reef scientists that accept as a baseline the state and coral reef cover that occurred at the beginning of their careers and use this to evaluate changes regardless of valid evidence of previously higher estimates.

In conclusion: The science certainly isn’t settled and I welcome this and future contributions by Sweatman et al and others on the matter. I started working on this problem about 7 years ago and I frequently ask more experienced scientists and old-timers what they remember from the 60s and 70s and what they think the baseline distribution for coral cover - which certainly varies among regions – really is.

We can’t know for sure without a time machine. But based on all the data at hand, I feel confident the GBR historically (before people starting mucking it up) had at least twice the coral it has now (including the nearshore reefs that we have lost and don’t even bother to survey anymore). This is pretty much what the vast amount of data (10,000+ surveys) for reefs around the world indicates has happened globally.

In Australia, this topic matters a lot because there has been an ongoing argument about how much the GBR has changed and how threatened it really is. Sadly, much of this is playing out in the dodgy Aussie newspaper, the Australian. See past debunking of this nonsense about the GBR being “blue again”here, here, here, here and here.

Both shifting baseline syndrome and data cherry picking are more common in hard science and the peer-reviewed literature that you’d think. I am working on a followup post about another case of coral reef scientists playing fast and loose with the data in an attempt to support a pet idea; in this case they exclude a different set of survey data in an attempt to make the opposite point Sweatman et al did, namely to argue that reef decline is worse than has been reported. So stay tuned…

Some background and disclaimers: The lead author, Hugh Sweatman is a colleague and collaborator of mine. We have published severalpaperstogether and are working on other collaborative projects and started corresponding about coral reef baselines about five years ago. Dr. Sweatman is the director of the long-term monitoring program at AIMS (the analysis was based on the dataset from this program). I was a reviewer of the manuscript and made the same points in my signed (non-anonymous) review that I made above. Finally, Sweatman et al (2010) directly criticized findings of a paper on which I was the lead author (Bruno and Selig 2007).

17 Responses to Coral Reef Baselines

John, snap! on the shifting baselines. I remember watching Jacques Cousteau talking about exactly the same thing decades ago. In one of his documentaries he had of footage showing what the corals reefs of the Red Sea and Haiti used to be like, and compared them with footage of the day (1980′s?). Not a pretty picture. Haiti of course was damaged because of silt run-off from the horrendous deforestation.

Fisheries scientists spin the same “delusional yarn” here in NZ, stocks are healthy blah, blah. But when I dive the vast schools of fish, that were regular features in many areas are gone. Sea grasses and kelp beds are either gone or silted over and dying, kina (sea urchin) are multiplying, and almost every amateur fisherman I speak to seems concerned about the decline in the fishery. It’s heartening when you hear some gung-ho person being genuinely worried about the environment, but not so heartening that it’s gotten to that stage that even they notice!.

Sweatman is right. The pre 86 data comes from here there and everywhere and does not have sufficient controls to be used for long term trends. Just look at the discontinuity at 1986. A first year biology student would reject the proposition.

Bruno also quotes the Pandolfi (2003)paper which using exceptionally flawed methods claim to show degradation of the reef. See

This comment is published in one of the worlds lowest rating journals because no other journal would touch it. Perhaps it is rubbish and I am barking up the wrong tree. You can be the judge.

Bruno also makes the mistake of using a satellite photo to infer significant sediment is reaching the GBR. The particular photo he uses is most likely to show a plume of dissolved organic matter and phyto plankton. NO smothering happening I am afriad although it is visually spectacular. Our own work over the years has shown that resuspension of sediment from the seabed is the biggest source of suspended sediment and that this resuspension has not changed since european settlement as the process is controlled by waves and an abundant source of fine sediment on the seabed that predates 1770.See also the work of Larcombe, Woolfe, Perry and Smithers. UNfortunately this geological work is mostly ignored by biologists who are trying desperately to show the GBR is knackered.

“Sweatman is right. The pre 86 data comes from here there and everywhere and does not have sufficient controls to be used for long term trends. Just look at the discontinuity at 1986. A first year biology student would reject the proposition.”

1) The data come from the peer reviewed literature not “here there and everywhere”. And as I said, were collected by well-known experienced scientists. If you are referring to the locations of the pre-86 surveys, well in population sampling, the more random the better, so “here there and everywhere” is a very good thing as it gives you greater ability to generalize, something you can’t really do with monitoring studies in fixed locations (a point I don’t think Hugh gets either).

2) Please address point 2 in the post as IMO it makes your argument irrelevant

3) “A first year biology student would reject the proposition” what “proposition”?

4) If you can’t be more professional and polite in your comments, they are going to get rejected

Bruno also makes the mistake of using a satellite photo to infer significant sediment is reaching the GBR. The particular photo he uses is most likely to show a plume of dissolved organic matter and phyto plankton. NO smothering happening I am afriad although it is visually spectacular.

You ‘selectively’ forgot to mention John’s comment on crown of thorns starfish. Here’s an extract from a recent paper from AIMS:

“The fact that primary A. planci outbreaks occurred on locations where floods intercepted large reefs on the GBR 3–5 years earlier shows that not only long-term chlorophyll concentrations but also large floods are a strong driver for A. planci primary outbreaks”

Here’s the real kicker from the abstract of that paper:

“…given plausible historic increases in river nutrient loads over the last 200 years, the frequency of A. planci outbreaks on the GBR has likely increased from one in 50–80 years to one every 15 years, and that current coral cover of reefs in the central GBR may be 30–40% of its potential value.”

What John Bruno said.

Our own work over the years has shown that resuspension of sediment from the seabed is the biggest source of suspended sediment and that this resuspension has not changed since european settlement as the process is controlled by waves and an abundant source of fine sediment on the seabed that predates 1770.

Here’s an extract from another paper with a co-author from your own department up at JCU that seems to suggest otherwise:

“For management this may be the most significant finding of this study, namely that land-based remediation measures that reduce the amount of riverine fine sediment inflow into Cleveland Bay would reduce the length of time when high turbidity prevails over seagrass and corals. Order of magnitude estimates suggest that if land-care management policies were implemented in the catchments of the Ross and Burdekin rivers to reduce by a factor of 4 the fine sediment discharge, the turbidity in Cleveland Bay would be halved after 170 days following cessation of river floods, which in turn would promote seagrass and reef growth.”

This geological work is mostly ignored by biologists who are trying desperately to show the GBR is knackered.

From what I can make of this, you are doing a pretty good job of cherry-picking both a) what you want choose to respond to here and b) which literature and data you want to make your (minority view) case that the GBR isn’t ‘knackered’ (despite your frequent claims in the media that the reef is in “bloody brilliant shape”).

This all seems like an argument about the details, trajectory and timing of coral decline on the GBR rather than the reality. Is anyone disputing seriously that at some time in the recent past, say in the last 150 years, coral cover on the GBR was probably above 50%? And this was, with no doubt a degree of variability, the ‘baseline’ value over the last say 2000 years (we don’t want to go to far back to when sea level was possibly going up and down a metre or two. Also all seem to be in agreement (Bellwood, Bruno, Sweetman – largely from the same data!)that coral cover across the GBR is currently about 20% (or maybe about 22% in the mid 2000s). So over the last 150 years or so there has been a decline from say 50% to 20%. We have a point in 1986 for which there seems some agreement (based also on mostly the same data set) that coral cover was about 30% (or 28% but the error bars are wide. We also know from the Sweetman et al paper that not unexpectedly the trends in coral cover vary across shelf and regionally and that there are obvious reasons for these differences in the variable stressors acting in these different places. So what the argument is about is the trajectory and timing of the decline and the causes. I think the trajectory before the 1980s will be difficult to ever determine accurately i.e. did cover decline linearly from say 1850 (first major anthropogenic terrestrial runoff issues) to 1986? or was there little decline say from 1850 to say 1950 and then a sharp decline from 1950 to 1986 driven more by crown of thorns outbreaks? There may be some arguments about the rate of decline from 1986 to present but the figures presented in Sweetman et al do not seem outlandish in any way. A 0.2% decline per year over the period I am suggesting from 1850 to 2010 gives an overall decline of 30%. The causes of the decline are surely reasonably accepted as terrestrial runoff, some effects of fishing and linked to these two crown of thorns outbreaks and more recently bleaching. The effects on coral cover of the loss of dugongs, turtles and other megafauna are more problematic but may be linked. If the argument is about the GBR being a well managed system because of the GBRMP and hence declines should not occur well think again. The only effective action taken by GBRMPA to address the issues of fishing, water quality and climate change did not occur until the 2000s with better fisheries management (especially of trawling), probably effective water quality management from 2008 with Reef Rescue and really nothing yet on climate change. Why would we expect the GBR to be different than say the Philippines except for the obvious point brought up by Hugh Sweetman in his paper that the GBR is subject to less stress because of position (well offshore) and low population and limited fishing. Personally I think these points are of limited relevance but that’s another story.

As its title suggests, the recent paper “Assessing loss of coral cover on Australia’s Great Barrier Reef over two decades, with implications for longer-term trends” by Steve Delean and Craig Syms and myself concerns the dynamics of coral cover over 19 years to 2004 on reefs across the Great Barrier Reef (GBR) province. The average coral cover declined over that time, and we try to identify the causes of decline by dividing the huge area into subregions and correlating the observed changes with known disturbance histories. We found that most of the decline was due to loss of coral in a minority of the subregions; coral cover in most subregions fluctuated but showed no substantial net change. This is one of the few documented examples of reefs showing cycles of disturbance and recovery that I have been able to find.

As a secondary issue, the extensive dataset gave an estimate of the rate of loss of coral across the GBR of 0.21% per year (95% CI: -0.10 to -0.33) over the study period, while Bellwood et al. (2004) show in their Figure 1a (reproduced below in John Bruno’s post) that average coral cover has halved from ~40% in the early 1960s to ~20% in 2000, more than twice the rate of decline. Bruno and Selig (2007) also used published studies from before the mid-1980s (which they listed) in their study and also found that cover on the GBR was markedly higher in earlier studies. We suggested some reasons why early values might be biased upwards and pointed out that the great majority of the later data came from AIMS manta tow survey that survey entire reef perimeters and so include zones of both high and low coral cover. The combination of the two types of data, confounded by time, in the one analysis is likely to increase the apparent rate of decline.

I would urge people who are interested to read the paper for themselves rather than rely on John Bruno’s recent post as a summary. In particular, readers can see for themselves whether we state, or even imply, that the GBR was substantially in the same pristine state as it was prior to European settlement up until AIMS surveys started. I maintain we do not and our paper is not very relevant to baselines for the GBR.

For real die-hards I have annotated John Bruno’s post below, giving my responses to many of his points

My annotations to John Bruno’s post Coral Reef Baselines

(John Bruno intorduces three studies that concern the longer term trends in condition of GBR reefs.)

JB: All three studies essentially concluded that GBR coral cover and overall ecosystem health began to decline decades ago, despite the fact that the GBR is currently in better shape than many of the world’s reefs.

JB: Sweatman et al dismiss pre-1986 data from all three studies, arguing that only AIMS survey data are suitable, and thus conclude that the GBR has changed little if at all due to human influences: “We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted”. Global climate change skeptics have frequently use a very similar approach: they rationalize cherry picking a favored data set and time interval in an attempt to show land and ocean temperatures haven’t increased, that sea ice hasn’t declined, etc.

Hey, hang on a minute! The sentence in boldface is a quote from the paper and I do believe that the GBR is currently less degraded from its natural, resilient state than some published reports (including one by John Bruno) have asserted, but that is not the same as stating that the GBR has changed little if at all due to human influences. There is no such statement anywhere in the paper by Sweatman et al. (while a number of anthropogenic changes that have affected the GBR are listed). Such a statement seems incompatible with the decline in GBR-wide coral cover clearly laid out in the abstract (reproduced in the post).

This last sentence is clearly an attempt to discredit by (rather irrelevant) association.

The topic of cherry picking is raised again later and addressed then.

JB: For several reasons listed below, I think the main conclusion of Sweatman et al is unsupported once you consider the scientific record as a whole.

1) There is much more pre-1986 data available than Sweatman et al suggest

JB: Our study alone (Bruno and Selig) includes data from 154 surveys of reefs across the Indo Pacific performed between just 1980 and 1982. We found that mean coral cover was 42.5% (95% CI, 39.3 and 45.6). Our analysis includes 104 GBR surveys performed between 1968 and 1983, all from published literature (see Fig. 2).

I am not at all sure what John Bruno’s point is here – the only data that we mention from prior to 1986 are exactly those used by Bellwood et al. (2004) and Bruno and Selig (2007).

2) Baseline data from other regions indicates that historically GBR coral cover was higher than it is today (or was in 1986

JB: In the Caribbean a small number (a few dozen) of reliable quantitative surveys from before the early 1980s suggest the regional mean for coral cover was 30-40% (Gardner et al 2003, Schutte et al 2010: see Figs. 5 and 6 below). Because countless well trained reef scientists were working throughout the region and observed the state of reefs over the last 100 years, most Caribbean reef scientists think that historically, the regional mean of Caribbean coral cover was higher than this; probably closer to 50% (or greater). Most Caribbean reefs of this era were dominated by Acropora spp., as can be seen in the photo below from 1974:

John Bruno is correct. My view would be that regional coral cover will depend on coral growth and on the local disturbance regimes. Even within the GBR province there are regions that suffer more tropical cyclones than others, based on recent decades (Puotinen 2004). One can see in Figure 2 of Sweatman et al. (reproduced above) that at least one reef on the GBR that was surveyed in 2004 had an average cover around the entire perimeter of more than 75%, but the mean around the perimeters of all the reefs surveyed that year was 22%. I would make no assertions about the Caribbean, the Philippines, Western Australian reefs or reefs anywhere other than the GBR.

JB: We also have substantially more older survey data for several non-GBR Pacific regions than are available for the GBR. For example, Gomez et al surveyed more than 600 sites in the Philippines in 1981 (Gomez et al 1981). Their work clearly shows a coral baseline far higher than today in the Philippines, the GBR or anywhere else in the world. Also see Fig. 4 below from Bruno and Selig (2010) that suggests the values reported in Gomez et al are representative of other regions at the time. And note the striking difference in the distribution of coral cover values among reefs between the early 1980s and for more recent surveys. Does it look like the Indo-Pacific as a whole, the Philippines or the reefs off mainland Asia haven’t changed? NO! They clearly have. ;Even assuming we had no pre-1986 coral cover data for the GBR, I don’t think it is logical to assume that the GBR hasn’t followed these global trends and that it has a much lower coral cover baseline than the rest of the world.

This is an interesting point, perhaps the most interesting point in this exchange. My view of global reef degradation is that it is due to the accumulated local impacts rather than some global process (though this is likely to change in the next decades as the oceans warm to critical levels). Growth of the human population would be one quasi-global factor and also a reason to distinguish the GBR from reefs in South Asia and the Philippines.

3) The GBR was already disturbed and changing by the time the AIMS monitoring program began

JB: AIMS began surveying a few dozen reefs along the GBR in 1986 after it became obvious that the reef ecosystem was changing due to over-fishing, sediment pollution from coastal development, ocean warming and predator outbreaks. Sweatman et al argue the values recorded by the early AIMS Long-term Monitoring Program (LTMP) surveys of the late-1980s, when cover was roughly 30%, are representative of the pre-human, historical baseline. I see no reason to assume this given the well-documented anthropogenic disturbances that were already affecting the reef by then (see Fig 1).

The AIMS monitoring program started in response to the second documented wave of Acanthaster outbreaks. But at no point in the paper do we state or imply that values we recorded were representative of any pre-human, historical baseline

4) Nearshore reefs were smothered by sediment from coastal development a century ago

Quite a few points about this section:

There is no doubt that inshore reefs are those most frequently exposed to the highest levels of runoff.

It is certainly true that other parts of the GBR are exposed on terrestrial influences less frequently (and at greater dilutions). Recent wet seasons have been atypically wet – the current season is probably going to be the wettest on record, associated with the strongest La Nina since 1974.

One reason why Dr Dekker’s observations are new and have not been detected previously on the water is that the far-reaching plumes are necessarily dilute. Why is that important? Well John Bruno points to the potential link between Acanthaster outbreaks and run-off (Fabricius et al., 2010). Based on my reading of that paper, the laboratory studies of larval survival and the model that is used to bring the components affecting Acanthaster population dynamics together both seem to require very high chlorophyll levels (as found on inshore reefs in the Wet Tropics region during the wet season) to prevail across the GBR in order to reproduce recent outbreak dynamics. This suggests that dilute runoff is unlikely to affect Acanthaster dynamics, though it may have other effects as yet unknown.

Cherry picking. The quote that John Bruno gives as an example comes from a section of the paper discussing coral dynamics and disturbances in those subregions of the GBR that showed a net loss of coral cover over the 19 years of surveys. Reefs in two of these, inshore regions near Cairns and Townsville, were badly bleached in 1998. In 2004, we made a large, systematic survey of the status of inshore reefs of the GBR involving 33 sites between Pt Douglas and Yeppoon (Sweatman et al. 2007). The surveys included measures of the densities of juvenile colonies. These data seem entirely relevant in that context of assessing recovery in those subregions.

As an aside, the results of systematic surveys of inshore reefs (Sweatman et al. 2007) surprised those who believed that most inshore reefs are now weedbeds or mudbanks. Average cover of hard coral (33%) on the inshore reefs (based on photo-transects) was slightly higher than on mid- and outer shelf LTMP reefs at that time (30%). The picture was certainly not all rosy, reefs in some subregions were clearly damaged and recovering slowly if at all, while others supported dense and diverse coral communities (a range of reef status rather like that among reefs further offshore that were the main subjects of our paper).

At least one (Havannah Is) of the 47 reefs that have been surveyed in some detail by the LTMP has had persistently high algal cover for more than seven years following loss of coral from bleaching and cyclone damage. To consider that representative of a majority would be cherry picking.

5) The early GBR survey data are sound

JB: Like Sweatmean et al, Bruno and Selig and Bellwood et al found that at a regional scale, average coral cover on the GBR has changed little since 1984 (see Figs. 1 and 2 above).

This is not surprising as the data from after 1986 that was used in all three studies are overwhelmingly from AIMS manta tow surveys.

JB: A similar pattern has been documented for the Caribbean, where substantial coral loss in the early 1980s changed to relative regional stasis since (Figs. 5A and C), i.e., a very similar pattern has been found in other regions (regardless of the scale of surveys and survey methods – also see Bruno and Selig for other Indo-Pacific examples) in which AIMS has never surveyed.

See my point under 2) (above) about accumulated local impacts rather than some global process.

6) Are the AIMS LTMP data sound?

JB: Here’s what Professor Mike Risk had to say about the AIMS monitoring program:

“One of the largest monitoring programmes is operated by the Australian Institute of Marine Sciences (AIMS) (e.g. Sweatman et al. 1998). Like all large monitoring programmes, it is expensive and time-consuming. It is designed to detect changes over time in reef communities at a regional scale. There has been a massive amount of data collected in this programme, which is commendable. On the other hand, as annual surveys are run between September and May, beginning in the north and working south, seasonal changes will be difficult to separate from spatial and temporal changes. It will take perhaps 30-50 years to accumulate enough baseline data to allow useful generalizations to be made” – (Risk 1999)

Professor Risk’s statement is incorrect: LTMP annual surveys do not and have never proceeded from north to south. The rest is a personal opinion that is not based on any familiarity with the AIMS data.

I am however intrigued by the idea of seasonal change in coral cover – are some corals deciduous??)

JB: The AIMS survey data presented in Sweatman et al used the “manta tow” technique; snorkelers are towed behind a boat, over a reef and visually estimate coral cover within 10m wide swaths to categories such as 0-5%, >5-10%, 10-20%, 20-30%, etc. I think the manta technique can be a valid tool for estimating crude spatio-temporal trends in coral cover. I even used the AIMS manta data in our Bruno and Selig paper, although I haven’t used it since (having spoken with several former AIMS technicians about the technique and it’s accuracy and precision). In short, Sweatman et al argue that their manta tow data is so superior to data from other sources, that only the AIMS manta data should be used to asses long-term trends in GBR state.

We do not argue that the manta tow method is better (though it certainly is different, see below). What is better, for the purpose of estimating GBR-wide coral cover, is the sampling regime: manta tows have been applied consistently on many reefs that are widely dispersed across the GBR province in each year.

JB: I disagree; not to knock the AIMS manta data, but it is a visual quasi-quantitative estimate collected by technicians as compared to the pre-1986 GBR data which was all collected by renouned PhD scientists, e.g., Endean and Stablum, Connell, Done, etc, that spent their lives studying the GBR.

This is a very inaccurate representation of the experience and expertise of the AIMS monitoring field team, who are full time employees (median length of employment >10 years) whose time is dedicated to monitoring, including at least 100 days a year at sea surveying reefs.

I would bet that a substantial fraction of the pre-1986 data were actually collected by technicians and research assistants for the lead scientists and authors of these studies – would that influence their validity?

JB: Furthermore, these pre-1986 GBR surveys were performed using wholly quantitative techniques such as underwater photography to estimate coral cover. I just don’t buy the argument that the AIMS-intern-manta tow data are superior to quantitative surveys by trained PhD scientists. For one, how can we know that the visual estimation of “20%” coral cover has stayed constant over time?

Consistency and quality control are fundamental to a long term program; the training and quality-control measures associated with the manta tow method are described or referred to in our paper. Readers should form their own opinions.

Do PhD scientists doing unrelated and often short-term projects ever compare their estimates for consistency between observers or over time?

Endean and Stablum (1973) made one of the largest quantitative surveys of coral cover prior to the mid-1980s, surveying 24 reefs between Townsville and Cairns using an innovative photo-quadrat method (very laborious in the pre-digital age). A series of photos of 1m2 quadrats were taken on transects that were generally laid at right angles to the reef crest. One of the reefs that they surveyed was John Brewer Reef near Townsville using two transects on the west flank (25m2) and 3 transects on the east flank (15m2) that were photographed over 3 days in 1971-72. Thus the coral cover estimate was based on 40m2 apparently placed haphazardly. John Brewer Reef is 6km long and has a perimeter of 15km (based on Google Earth). This is not extensive sampling for the purpose of estimating GBR-wide coral cover (which was not its intended purpose). Estimates for several of the 24 survey reefs were based on less than 10m2.

JB: Secondly, I really doubt any technique only capable of estimating coral cover to the nearest 10% (i.e., with such low precision) is sensitive enough to even detect the gradual decline in coral cover that has been reported for the GBR and elsewhere, e.g., ~0.5-2% a year. (Just take a look at the error bars in Fig. 2 from Sweatman et al in the Abstract above). Third, I doubt the AIMS manta surveys were run long enough to detect regional trends without including data from other sources. Given the inherent noise in the system, I usually look for 30+ years of data before I try to test for a large-scale trend.

Does this really refer to Sweatman et al. (2011)?? The first paragraph of the results section reads as follows:

“Based on all the reefs monitored in each year, the average cover of living coral on GBR reefs declined from 28.1% in 1986 to 21.7% in 2004 (Fig. 2). The average rate of loss based on the linear model was 0.21% cover per year (95% CI: -0.10 to -0.33). However, such net decline was by no means general across the ~345,000 km2 of the GBR. Changes in coral cover varied across the GBR region (Fig. 3); the coral cover on inshore reefs declined by 0.32% per year (95% CI: -0.0007 to -0.64), coral cover on mid- shelf reefs declined by 0.30% per year (95% CI: -0.16 to -0.45), and there was no net change in coral cover on outer shelf reefs (rate of change = 0.002% per year, 95% CI: 0.2 to -0.20). As I read that, AIMS manta tow data must be sensitive enough because we did detect gradual declines (eg confidence limits for the rate of change did not include zero) at several spatial scales and clearly state as much in the results.

Incidentally, if you read the caption to Figure 2 of Sweatman et al. (reproduced in JB’s post)), it states clearly that the whiskers represent the range of data values – they are not error bars.

JB: Fourth, I think it is somewhat misleading to represent the manta tows as having far greater spatial coverage. This is only true if you compare the cumulative area of the samples. However, unlike the manta tows, quantitative benthic reef surveys include extensive independent replication and if properly designed will produce coverage estimates that are representative of the broader surrounding benthos.

It is not so much the manta tows as the manta tow surveys that have greater spatial coverage. One could sit down and plot out the survey sites for each year since 1960 on a map, but as a short cut, Bruno & Selig (2007) identified 104 surveys on the GBR in the 16 years 1968-83, giving an average of 6.5 surveys per year. Our analysis was based on reefs that were surveyed more than once in the 19 years, giving between 72 and 189 reefs per year (median = 99). In addition the LTMP survey reefs were intentionally widely dispersed across the GBR province. Thus for estimating change in GBR-wide coral cover, the reefs are the replicates, they are widely dispersed across the geographic area of interest and there quite a few reefs were surveyed in this standard way each year for 19 years.

JB: Finally, I suspect that the manta technique substantially underestimates coral cover because it does not (and cannot) correct for uninhabitable (by corals) substrate that is encountered in surveying. When coral scientists use the term “coral cover”, they mean the percentage of the sea floor occupied by stony corals that is habitable by this group, i.e., hard substrate, not sand or other types of soft substrate. This is easy to factor out with other quantitative survey methods; you just divide the total coral cover by the total hard (suitable) substrate cover to calculate “coral cover”. In most cases, the hard/suitable cover is nearly 100%. But because manta tows cover wide and long swaths of reef, they inevitably include small and large patches of sand, etc, and it is impossible to do the mental math to factor this out when estimating the coverage of corals and other benthic taxa while getting pulled behind a boat in shark infested waters! (manta towing is a job for the young and immortal!) If you compare the AIMS manta data to the quantitative AIMS video transect data (~48 reefs surveyed annually) you can see this artifact: from 1994-2003 the mean coral cover from the AIMS manta tows was 21.7 +/- 0.5 (1 se) and 30.7 +/- 0.9 from the video transects. This suggests that the drop in GBR coral cover in the mid-1980s could be due to a methodological bias of the manta tow technique. Would this mean that the GBR hasn’t lost any coral or that “losses of coral in the past 40–50 years have probably been overestimated”? Only if you think that the coral cover baseline, unlike the rest of the world, for the GBR is only ~30%: as I explained above, I think this is unlikely.

compare John Bruno’s statement just above:

This suggests that the drop in GBR coral cover in the mid-1980s could be due to a methodological bias of the manta tow technique.

with the following passage from the discussion section of Sweatman et al:

Most cover estimates for GBR reefs in any year after 1986 came from AIMS monitoring surveys of the entire reef perimeters of a large number of widely dispersed reefs and so were based on a swathe 10m wide and several kilometres long that spanned reef zones with both high and low coral cover. The apparent abrupt drop in average coral cover on the GBR in 1986 is most probably due to the inclusion of AIMS monitoring data with cover estimates from small selected patches of reef from small-scale studies.

We seem to be agreeing violently ….

OK so logically, it does not matter whether the small scale surveys give an accurate estimate of GBR-wide coral cover and the manta tows underestimate it or the manta tows give accurate values and the small scale studies are biased upwards, the important point is the difference and the result in either case will be an overestimate of the slope of decline since the 1960s and 70s. This means at least two things:

1. losses of coral in the past 40–50 years have probably been overestimated.

2. If losses have been overestimated, the GBR is currently less degraded from its natural, resilient state than some published reports have asserted

7) Other skepticsoundbites

JB:Sweatman et al make a lot of noise about variation among reefs and subregions in coral cover trajectories and states. Basically, there is a high degree of spatio-temporal asynchrony in the system, as we discussed in Bruno and Selig and illustrated with this graphic: (Fig. 7 from Bruno & Selig)

This is a nonsensical statement given that Sweatman et al. detected and reported a decline in coral cover.

JB: Climate change deniers use this argument frequently, suggesting that natural short term variation makes long-term, anthropogenically forced trends, unlikely or undetectable. This is in a sense what Sweatman et al are arguing as well.

See above.

JB: But the fact that there is great;unforced spatiotemporal variation, i.e, noise or weather, does not mean that longer-term, human-induced change isn’t also happening. (Although this is indeed a big issue for many fields of global change science: how to detect slow, long-term trends in a sea of shorter term noise.)

JB: Sweatman et al: A reef system that is stable in the long term will still show cycles of disturbance and recovery at a subregional scale.

JB: True, but so will a reef system that isn’t stable and is declining as has been shown for other regions such as the Caribbean (Schutte et al 2010).

Also true.

And so on…..

(I wrote this and submitted it to Ove HG to post on 16 Feb; after all this HTML fiddling I know why he did not find time to post it)

Thanks for the useful reply. And apologies for any delay – I had thought that you would be interacting with John (Bruno) and that you would be sending your discussion items to him to post as well as me. I had a big week in my day job and I didn’t get to the bulk of my e-mails until now (weekend) – so am sorry if you felt that I was delaying things here deliberately, because I wasn’t.

I have edited out the more nasty and unprofessional aspects of Hugh’e response. If he wants to resubmit that content, rewritten in a more adult manner, he is welcome to do so. Please stick to the facts and avoid making subtle personal accusations Hugh.

“In particular, readers can see for themselves whether we state, or even imply, that the GBR was substantially in the same pristine state as it was prior to European settlement up until AIMS surveys started. I maintain we do not and our paper is not very relevant to baselines for the GBR.”

If that is now the case, I think we’ve got no disagreement. What led me to the belief that you were, was statements like this: “We argue that much of the apparent long-term decrease results from combining data from selective, sparse, small-scale studies before 1986 with data from both small-scale studies and large-scale monitoring surveys after that date. The GBR has clearly been changed by human activities and live coral cover has declined overall, but losses of coral in the past 40–50 years have probably been overestimated.”

But if you now concede that “our paper is not very relevant to baselines for the GBR.” then I think Iv’e achieved more than I could have hoped with this post.

Although I’m still curious about your views about the GBR baseline, eg, your agreeing with my point that; “Sweatman et al are effectively arguing that the GBR has naturally lower coral cover (averaging a mere 28%) than the Caribbean, which lacks plating species; even in dense thickets of branching Acroporids (as seen above), Caribbean coral cover rarely exceeds 70% whereas on the GBR, cover can easily reach 100% (see the photo below).”

And I’m puzzled by your new found contempt for meta-analysis; you seemed supportive when invited to coauthor papers using them, eg. Bruno et al 2007 and Bruno at al 2009.

In his post, John Bruno ultimately accepts that “… the drop in GBR coral cover in the mid-1980s could be due to a methodological bias of the manta tow technique.” I think this is a methodological issue but really concerns meta-analyses.

In his post, John Bruno refers more than once to the perception by Sweatman et al. that AIMS monitoring data are superior to those from other sources (which we think should be ignored). Neither of these points is true. I do not think it is the quality of the available data that is the main issue, it is the use of the data in some recent studies. Here is a “cherry picked” example: Bellwood et al. (2004) inexplicably did not give any details of their data sources or analyses, other than that the data are from published sources. Their Figure 1a (the first figure in John Bruno’s post) shows “coral cover on the GBR” plotted against time. The earliest data point in the plot appears to be from 1963. Reef ecology is a young science and among published studies, that data-point can only be from Joe Connell’s study at Heron Island. Joe Connell is a most distinguished ecologist, his studies at Heron Island Reef have been invaluable and most influential as long-term studies of the dynamics of coral communities. He started the study on a small scale and his initial plots that were surveyed in 1962 and 1963 amounted to 11 m2 of reef area (Connell et al. 1997). Small areas may be appropriate for careful studies of community dynamics, but one does not need a PhD to grasp that 11 m2 from just one reef in the far south of the Great Barrier Reef (GBR) province is unlikely to provide a reliable estimate of average coral cover on the nearly 3,000 reefs spread over 335,000 km2 of the GBR in that year. The relative emphasis given to that point in any analysis of changes in coral cover clearly needs to be adjusted accordingly.

In my view, the drop in coral cover over 50-odd years has not been overestimated because of an inadequacy of the manta tow technique, the overestimate came about because a large body of manta tow data (with its associated strengths and weaknesses) was mixed with earlier estimates of coral cover by other methods into over-simplistic meta-analyses. In the un-cut version of my comment, I referred to a quip from an editorial on meta-analyses in the medical literature (DeMaria 2008) which John Bruno deleted, along with this whole section. I found it amusing, but it may offend some; readers can form their own opinions. Dr De Maria was commenting on the rapidly increasing number of studies using meta-analyses (compilations of results from several separate studies to address a question) in that field, and ruminating on some strengths and weaknesses of such analyses (- just one of many such discussions in the literature). One of the commonly listed traps for the unwary in meta-analyses is mixing up of quite different types of data (especially if these are confounded in time). Graphs like Figure 1a of Bellwood et al. would make any alert person ask “What on earth happened to the coral on the GBR in 1986?” Such a graph should ring very loud alarm bells in the minds of meta-analysts (and peer-reviewers).

I am not contemptuous of meta-analyses, but I freely confess I am a sceptic, and the case in point is an example of why.

I’ve been thinking about Hugh’s response and paper. He is right about two things: I mistakingly assumed the error bars in his graphic were, well, error bars and not “range” bars (I’ve never seen data range used as an error term in a graph). He is also right that the AIMS manta tow surveys did detect a declining trend.

Hugh is wrong about a few things too. However well trained AIMS techs are, there simply is no way to ensure visual estimations of community structure do not change over time. The estimations are based on perception which is obviously not a static element. Hugh points out that AIMS techs spend 100 days a year at sea. Awesome! I spend 365 days a year on land, but that doesn’t mean my perceptions about things – beauty, weather, food, language – don’t change. Hugh is also wrong in arguing that it is necessary to apply such consistency tracking when using quantitative measures of coral cover, eg, “Do PhD scientists doing unrelated and often short-term projects ever compare their estimates for consistency between observers or over time?” No they don’t, because there are not any “observers”, there is a value of measurement, which is not based on observed perceptions.

Hugh makes the point that the sample size of the pre-AIMS, pre-1986 survey data (~100 reefs/surveys) is too small to accurately describe the state of the GBR. Perhaps. Yet the whole thesis of Hugh’s paper is that the post-1986 surveys data somehow tell us about the GBR in earlier decades, ie, when the sample size is zero! I can accept as a reasonable opinion the argument that we don’t have enough data to reliably estimate GBR coral cover pre-1986. But to argue that data collected between 1986 and 2004 does tell us about reef state in the 1960s, 1970s and 1980s but data collected during those periods do not, seems dubious to me.

Yet all of this is, I think, largely irrelevant. What I care about – what I’m interested in- is, as the title of the post implied, coral reef baselines. What was natural and how much have reefs changed from that pre-human state.

Hugh thinks that I have misrepresented the arguments regarding the baseline in Sweatman et al 2011:

From his comments;

“I would urge people who are interested to read the paper for themselves rather than rely on John Bruno’s recent post as a summary. In particular, readers can see for themselves whether we state, or even imply, that the GBR was substantially in the same pristine state as it was prior to European settlement up until AIMS surveys started. I maintain we do not and our paper is not very relevant to baselines for the GBR.”

“JB: We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted”. Global climate change skeptics have frequently use a very similar approach: they rationalize cherry picking a favored data set and time interval in an attempt to show land and ocean temperatures haven’t increased, that sea ice hasn’t declined, etc.”

“Hey, hang on a minute! The sentence in boldface is a quote from the paper and I do believe that the GBR is currently less degraded from its natural, resilient state than some published reports (including one by John Bruno) have asserted, but that is not the same as stating that the GBR has changed little if at all due to human influences. There is no such statement anywhere in the paper by Sweatman et al. (while a number of anthropogenic changes that have affected the GBR are listed).”

Maybe. I will paste the relevant passages from Sweatman et al 2011 below and ask Hugh to explain what he means by “We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted.”

If the data and discussion in Sweatman et al is as Hugh says “not very relevant to baselines for the GBR” how did he come to this conclusion? What does he think was natural? How much has the GBR changed? There must be a secret AIMS estimate somewhere, otherwise how could Sweatman et al 2011 have determined that previous estimates are inflated? I’ve said what I think based on the evidence at hand. What does Hugh think?

——–

“We argue that much of the apparent long-term decrease results from combining data from selective, sparse, small-scale studies before 1986 with data from both small-scale studies and large-scale monitoring surveys after that date. The GBR has clearly been changed by human activities and live coral cover has declined overall, but losses of coral in the past 40–50 years have probably been overestimated.”

“Subheadings in the Discussion: Long-term changes in coral cover on the GBR and How much is the GBR degraded?”

“Whatever levels of coral cover existed prior to 1986, the homogeneous data series from the long-term monitoring programme shows firstly that the average cover on the perimeters of reefs across the GBR declined from 28.1 to 21.7% between 1986 and 2004 and secondly that this has been mainly due to large declines in some subregions rather than a consistent, system-wide decline.”

“We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted.”

There’s an extraordinary amount of effort that’s obviously gone into this and I’m gratefully you make it publically available.

Look I’m in total agreement with you on a couple of things

1) Your paper is not about baseline. It’s really hard for me to fathom how John comes to that conclusion. It seems to revolve around this sentance. “We argue that the GBR is currently less degraded from its natural, resilient state than some published reports have asserted.”. I read it as a critical comment on the ability of previous meta-analysis to capture the degradation process rather than a statement on the natural state per se.

2) The repeated association of your work with the tactics and techniques of dis-informing skeptics/deniers is extremely unnecessary. I read it as you did as guilty by association. Apart from that it sheds absolutely no light on the nature of your scientific dis-agreement. John chastised you for unprofession original post but I think he should try a little introspection.

3) This is essentially a disagreement about how to handle data. The shift in mean and SD in Fig 1a coupled with the knowledge that this represents a shift in data source makes it pretty obvious this is all about data handling.

It would have been interesting to see the un-edited verion of Hugh’s post because on Skepticalscience I was most critical of the approach John had taken in his article. While there is a genunine scientific disagreement here I think John too readily strays into the wider climate change debate with his article. He seems to have one eye on the overall message, is concerned how The Australian newspaper is going to twist your results. Obviously this is well outside the science but I’m interested in whether you think the wider issues are imposing constraints on what are acceptable conclusions to draw?

One final thing John you write

“But if you now concede that “our paper is not very relevant to baselines for the GBR.” then I think Iv’e achieved more than I could have hoped with this post.”

This really sums up the problem I have with your reading of Hugh’s work. “now concede” – the whole point is that at no time was he proposing baselines. His point seems to be that previous meta-analysis (yours included) can’t tell us anything about baseline. Rather than reflect on a perceived victory what you really should be doing is critically assessing your own work in light of the critique. I realise you’ve been doing that and it seems your way forward is to drop the AIMS data from future work. It still seems the longest, most wide ranging, consistently driven assessment of the GBR that exists. I wonder whether it sensible to take that approach?

“Hugh is wrong about a few things too. However well trained AIMS techs are, there simply is no way to ensure visual estimations of community structure do not change over time.”

If your aim is perfection then this is true but there are ways of minimising this. Training, SOPs, independant re-checking , consistency in leadership, goals and intent and so on. All these seem to be in place at AIMS. Human error is a feature of all science, how do you know a photo from 40 years ago isn’t mis-labelled? This is a question of applying the same stringent assessment to all the data.

[...] The third category of information comes from long-term survey data. The Australian Institute of Marine Science began annual ecological survey of key aspects of coral and fish abundance on the Great Barrier Reef in 1986. While these surveys biased toward offshore reef areas and hence have probably not caught the full picture of human impacts on the Great Barrier Reef, they are empirically sound in terms of the methodology needed to examine ecological parameters such as coral abundance over time. As indicated above, there has been some scientific debate (which always goes on and is part of the sceptical process of science) and some of the details have been discussed by Professor John Bruno in separate postings to SkS and Climate Shifts. [...]

While performing a random search on the topic of reef rehabilitation, I came across this discussion. I followed it with great interest, and then suddenly discovered that I was involved in it. This thread is by now so old that the chances are excellent no one will read what I post here, which is fine by me. Nonetheless, some comments are in order.

I agree with John’s admonition that we should conduct ourselves with courtesy and consideration, in a collaborative spirit. There is enough acrimony in politics today that we need not introduce any more into science.

I note that Hugh deals very dismissively with my comments on the AIMS monitoring program-which themselves are by now very old. Perhaps he might have wondered from where I got the information… My comments were almost a direct quote from one of the most senior scientists at AIMS, who knows a great deal about that program. He chose to remain anonymous because he feared the sort of reaction which in fact eventuated.

Mixed in with the various elements of this thread were comments from Hugh that we need to pay more attention to the geological literature [a noble goal], as well as his dismissing some of the evidence of transport of terrigenous material out onto the GBR shelf. In fact, almost 20 years today this subject was covered in a “geological” paper that showed long-range transport of material important to corals: “terrigenous influence on diet is measured out to the edge of the continental shelf, circa 110 km offshore” [Risk et al. 1994: MEPS 106: 121-130].